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Sample GSM510545 Query DataSets for GSM510545
Status Public on Feb 17, 2010
Title HCF-DS12491
Sample type RNA
Source name Human Cardiac Fibroblasts
Organism Homo sapiens
Characteristics cell type: Human Cardiac Fibroblasts
Biomaterial provider ScienCell;6300
Growth protocol Followed vendor recommendations for growth protocol/media
Extracted molecule total RNA
Extraction protocol At cell harvest, a subset of cells was stored at -20oC in RNALater. Total RNA from 5 X 10^6 cells were purified using Ribopure (Ambion) according to vendor recommended protocols. Total RNA quality was assessed on RNA 6000 Nano Chips (Agilent) using a Bioanalyzer (Agilent).
Label biotin
Label protocol A Whole Transcript Sense Target Labeling Assay (Affymetrix) was used to reduce the rRNA, perform in vitro transcription (IVT) and create labeled sense strand DNA for hybridization to the arrays.
Hybridization protocol Hybridizations were carried out according the manufacturer (Affymetrix) protocol
Scan protocol Affymterix Gene Chip Scanner 3000
Description Human Cardiac Fibroblasts
Data processing Intensity files from the scanned exon arrays were analyzed at the exon level (Affymetrix ExACT 1.2.1 software). Sample data were quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized
Probe group file used for analysis: HuEx-1_0-st-v2.r2.pgf
Submission date Feb 17, 2010
Last update date Apr 23, 2013
Contact name ENCODE DCC
Organization name ENCODE DCC
Street address 300 Pasteur Dr
City Stanford
State/province CA
ZIP/Postal code 94305-5120
Country USA
Platform ID GPL5188
Series (1)
GSE19090 Exon arrays of ENCODE tier 1, tier 2 and tier 3 cell types

Data table header descriptions
VALUE quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized

Data table
2315101 35.5022
2315102 25.99617
2315104 16.58973
2315105 49.63651
2315107 72.58772
2315114 12.24242
2315126 3.590777
2315132 3.650275
2315133 65.0116
2315134 3.737581
2315138 47.82121
2315140 18.70402
2315142 2.245458
2315144 9.643749
2315146 7.635934
2315148 61.91059
2315149 38.63684
2315150 71.10081
2315151 11.07299
2315153 14.26179

Total number of rows: 1384231

Table truncated, full table size 23040 Kbytes.

Supplementary file Size Download File type/resource
GSM510545_X_Hs_HCF_E_091208_09_DS12491_W.CEL.gz 21.5 Mb (ftp)(http) CEL
GSM510545_wgEncodeUwAffyExonArrayHcfSimpleSignalRep2.broadPeak.gz 21.0 Mb (ftp)(http) BROADPEAK
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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